Search Results for 'model organisms'


January’s issue of Cold Spring Harbor Protocols wraps up the second volume of our ongoing Emerging Model Organisms series. The idea behind the series is that technical advances have allowed for great expansion in the range of organisms used for research. Each set of articles is meant to introduce the reader to a new organism, to explain why it’s useful for laboratory research and to provide information on husbandry, genetics and genomics, and a set of basic laboratory protocols. The first set of 23 emerging model systems was collected in a laboratory manual, and the current set of 18 will soon be as well. January’s organisms are:

The Rabbit (Oryctolagus cuniculus): The rabbit is a valuable animal model for a variety of biomedical research areas including in vitro fertilization, early embryology and organogenesis, neurophysiology, ophthalmology, and cardiovascular research. The rabbit is also used as a model for toxicology studies and analyses of drug effects on embryo and fetal development, as well as for research involving the immune system, not to mention its common use in antibody production. Christoph Viebahn and colleagues from the University of Göttingen provide an overview of the rabbit as an experimental system, and protocols for mating and embryo isolation, dissection and fixation of embryos, embryo culture, staining and imaging, immunofluorescence, in situ hybridization, mounting, embedding and sectioning, embryo transfer, artificial insemination and cryopreservation of embryos.

Paramecium tetraurelia: Paramecium makes an interesting unicellular model, as the authors note:

Paramecium tetraurelia is a widely distributed, free-living unicellular organism that feeds on bacteria and can easily be cultured in the laboratory. Its position within the phylum Ciliophora, remote from the most commonly used models, offers an interesting perspective on the basic cellular and molecular processes of eukaryotic life. Its large size and complex cellular organization facilitate morphogenetic studies of conserved structures, such as cilia and basal bodies, as well as electrophysiological studies of swimming behavior. Like all ciliates, P. tetraurelia contains two distinct types of nuclei, the germline micronucleus (MIC) and the somatic macronucleus (MAC), which differentiate from copies of the zygotic nucleus after fertilization. The sexual cycle can be managed by controlling food uptake, allowing the study of a developmentally regulated differentiation program in synchronous cultures. Spectacular genome rearrangements occur during the development of the somatic macronucleus. Their epigenetic control by RNA-mediated homology-dependent mechanisms, which might underlie long-known cases of non-Mendelian inheritance, provides evolutionary insight into the diversity of small RNA pathways involved in genome regulation. Being endowed with two alternative modes of sexual reproduction (conjugation and autogamy), P. tetraurelia is ideally suited for genetic analyses, and the recent sequencing of its macronuclear genome revealed one of the largest numbers of genes in any eukaryote. Together with the development of new molecular techniques, including complementation cloning and an easily implemented technique for reverse genetics based on RNA interference (RNAi), these features make P. tetraurelia a very attractive unicellular model.

Eric Meyer and colleagues from the CNRS have written an overview of P tetraurelia as a model system, and protocols for maintaining cell lines, mass culture, gene silencing, DNA microinjection, immunocytochemistry, and fluorescence in situ hybridization.

We have some new organisms in the works for Volume 3, but would welcome your suggestions.

We’re getting toward the end of the second volume of our Emerging Model Organisms series in Cold Spring Harbor Protocols, and November’s issue brings us a look at the Hawaiian Bobtail Squid and the genus Dioscorea, or True Yams.

Euprymna scolopes, the Hawaiian Bobtail Squid (our cover model this month, see below) is a cephalopod that’s well-suited for study in the laboratory. E. scolopes is primarily studied in three contexts:
1) as a model for cephalopod development–the embryos and protective chorions are clear, making it amenable for the observations and manipulations common in other studied model systems
2) as a model of animal-bacteria symbioses with the luminous marine bacterium Vibrio fischeri
3) as a system for studying the interaction of tissues with light, as the squid features a specialized light organ.

Heinz Gert de Couet and colleagues supply an overview of the Hawaiian Bobtail Squid as a model system, along with protocols for Preparation of Genomic DNA, Confocal Immunocytochemistry, Whole-Mount In Situ Hybridization (parts 1 and 2), and Culture and Observation.

Dioscorea is a large genus of plants that are monocots but that look like dicots, and are closely related to the phylogenetically derived group containing the grasses. It’s interesting evolutionarily because of the position it occupies, as a link between the eudicots and grasses–groups that contain all the model flowering plant species. The true yam is also important as a food crop. R. Geeta and colleagues provide an overview of the genus, and protocols for husbandry, culturing tissues, management of plantlets, controlled crosses, and DNA extraction.

CSH Protocols November Cover

CSH Protocols November Cover

Volume 2 of our Emerging Model Organisms series rolls on in the October issue of Cold Spring Harbor Protocols. This month brings a look at two emerging models, one all-time classic.

Neelima Sinha and colleagues present “The Mother of Thousands” (Kalanchoë daigremontiana), a plant which has the fascinating ability to regenerate and entire organism from somatic cells. The process of forming a somatic embryo outside of a seed environment provides an attractive model system for studying embryogenesis. Kalanchoë is also used in the study of Crassulacean acid metabolism (CAM), which is an important evolutionary adaptation of the photosynthetic carbon assimilation pathway to arid environments. In addition, natural compounds extracted from tissues of Kalanchoë have potential applicability in treating tumors and inflammatory and allergic diseases, and have been shown to have insecticidal properties. Protocols are provided for fixing and sectioning tissues, in situ hybridization, transformation using agrobacterium, DNA extraction and RNA extraction.

John Werren and colleagues provide The Parasitoid Wasp Nasonia: An Emerging Model System with Haploid Male Genetics. Nasonia is a genus consisting of four interfertile species. They’re particularly useful as a genetic tool for study because females are diploid and develop from fertilized eggs, and males are haploid and develop from unfertilized eggs. This allows geneticists to exploit many of the advantages of haploid genetics in an otherwise complex eukaryotic organism. Protocols are available for field collection, strain maintenance, rearing fly hosts, egg collection, virgin collection and crossing methods, larval RNAi and curing Wolbachia bacterial infections.

As for that “classic” system mentioned above, if you know genetics, then you know Barbara McClintock, and you know that Maize has been a keystone model system for nearly a century. Micheal Scanlon and colleagues have written up Maize (Zea mays): A Model Organism for Basic and Applied Research in Plant Biology, which gives an up-to-date discussion of the state of Maize research.

Our long-running series of articles highlighting emerging model organisms continues in September with three entries, The Starlet Sea Anemone (Nematostella vectensis), Cephalochordates (Amphioxus or Lancelets) and The Western Clawed Frog (Xenopus tropicalis).

The slow rate of sequence evolution, the presumed high degree of preservation of ancestral traits, the ease of culturing, and the availability and experimental tractability of the early embryos have made Nematostella a prime cnidarian model for a number of biological studies. It serves not only as a model system for cnidarians, but also as an important representative of its phylum in comparisons with other lower Metazoa or Bilateria. Ulrich Technau and colleagues provide an overview of Nematostella, and protocols for spawning, in situ hybridization, antibody and phalloidin staining and BrdU labeling.

Cephalochordates, commonly called amphioxus or lancelets, are marine invertebrate chordates. Studies on cephalochordates have answered some long-standing questions concerning the evolution of vertebrates from their invertebrate ancestors and have also generated interesting avenues for further investigation of the evolutionary origin of developmental mechanisms that led to the emergence of the vertebrate body plan. Linda Holland and colleagues provide background on Cephalochordates, along with detailed methods for Amphioxus embryo collection, in situ hybridization, DNA extraction, and RNA extraction and extracting RNA from small amounts of tissue for RT-PCR.

Xenopus tropicalis is a small, wholly aquatic frog that is a diploid relative of Xenopus laevis. It shares many of the advantages of X. laevis as a model organism for studying aspects of vertebrate biology, particularly the genetic, biochemical, and environmental factors that influence vertebrate development from embryonic stages through adulthood. X. tropicalis is also finding uses as an important test species for assessing the impact of environmental toxins and disease on amphibians, which are in decline in many areas of the world due to water-borne pollutants and infectious agents such as the chytrid fungus. Frank Conlon and colleagues have contributed an overview of X. tropicalis, along with protocols for natural mating, in vitro fertilization, and tissue sampling and genomic DNA preparation.

May’s issue of Cold Spring Harbor Protocols saw the publication of the final two species from Volume I of our “Emerging Model Organisms” series. These articles have been collected and made available as a laboratory manual. June’s issue brings us the first species from Volume II, the Honeybee (Apis mellifera).

Because of their obviously important role in pollination, a great deal of recent research has gone into investigating diseases which affect honeybees, such as Colony Collapse Disorder. Bees also exhibit remarkable social behavior, complex learning and memory and language skills, making them an excellent system for neuroscience research into these topics. The haplo-diploid sex determination system of bees is also of great interest. The sequenced genome of honeybees has allowed for comparisons with other species, with some surprising results. The genes underlying circadian rhythms in bees are much more like those in mouse than those found in Drosophila. The same goes for DNA methylation in gene regulation, where bees, like mammals but unlike Drosophila, methylate DNA on CpG residues.

Protocols are provided for Fixation and Storage of Honeybee Tissues, Whole-Mount In Situ Hybridization of Honeybee Tissues, In Situ Hybridization of Sectioned Honeybee Tissues, Immunohistochemistry on Honeybee Embryos, and RNA Interference (RNAi) in Honeybee Embryos.

Each month’s issue of Cold Spring Harbor Protocols will feature new (and newly revisited) model organisms, and the next set will be collected in Volume II of the manual series, out some time early next year.

May’s issue of Cold Spring Harbor Protocols marks the end of Volume I of our collection of material on Emerging Model Organisms. The final two featured organisms are the bichirs and the African butterfly.

The lineage leading to the teleost fishes, like the zebrafish, has undergone a whole-genome duplication, and there are many differences in the molecular and cellular mechanisms of embryogenesis between teleosts and other actinopterygians (ray-finned fishes) and sarcopterygians (fleshy, or lobe-finned fishes). Polypterus (bichir) is a taxonomic order of fish that diverged from all other actinopterygians ~400 million years ago during the Devonian period, soon after the divarication of an ancestral bony fish into Actinopterygii and Sarcopterygii. Polypterus share several characteristics of cartilaginous fishes and basal bony fishes. Bichirs exhibit holoblastic cleavage, like that seen in amphibians, and different from the meroblastic cleavage of teleosts. As such, it makes for an excellent system to study ancestral states and the divergence of embryonic processes in teleosts and amphibians. The Genus Polypterus (Bichirs): A Fish Group Diverged at the Stem of Ray-Finned Fishes (Actinopterygii) presents an overview of bichirs, and protocols for microinjection and whole-mount in situ hybridization are also available.

The African Butterfly Bicyclus anynana is a valuable model organism for a variety of reasons. A range of phenotypes are readily examined, such as wing color patterns (including eyespots), seasonal forms, male androconia (secondary sexual traits), and a range of life-history traits (relevant to aging research). Many of the phenotypes are directly related to the drastically different environments found during the dry and wet seasons in East Africa, offering an opportunity to study adaptation to environmental conditions. The genus Bicyclus and closely related genera are highly speciose, giving a great variety of closely related species for diversity studies. B. anynana is small and can be reared in large numbers. The African Butterfly Bicyclus anynana: A Model for Evolutionary Genetics and Evolutionary Developmental Biology provides an overview of the species as a model system. Protocols are available for culture and propagation, surgical manipulations, grafts, fixation and dissection, wing dissection, in situ hybridization, immunohistochemistry (embryos), immunohistochemistry (wings), analysis of pheromones, fat content and weight, respirometry, hemolymph extraction, and injection of chemicals.

As noted, this completes the first set of Emerging Model Organisms, and the collected articles are available in a laboratory manual. The second volume begins next month, and the list of species is available here.

April’s issue of Cold Spring Harbor Protocols introduces, well, re-introduces two longstanding experimental model systems, the snail (Ilyanassa obsoleta) and the leech (Helobdella).

The use of Ilyanassa in the laboratory dates back to the 1890’s, and it was a favorite of Thomas Hunt Morgan’s in the 1930’s. As a member of the Lophotrochozoa, a group made up of nearly one third of the animal phyla, the snail exhibits a spiralian developmental program. In addition to its use to study spiral cleavage, Ilyanassa is also used to study asymetric cell division and other phenomena:

It is an important model for studies of metamorphosis, the ecology of parasitism, and imposex, a striking morphological disorder caused by the disruption of sexual endocrine systems by environmental contaminants. Ilyanassa is also useful for studies of comparative neurobiology.

Protocols are provided for Obtaining Embryos, Induction of Larval Metamorphosis, Fixation, Isolation of Genomic DNA, Protein Isolation, and Pressure Injection.

In the 1870’s, C.O. Whitman, director of the MBL at Woods Hole used a local leech species for developmental biology studies. Gunther Stent’s lab used leeches for neurobiology research in the 1970’s. Like Ilyanassa, leeches are Lophotrochozoans and exhibit spiral cleavage and thus are useful species for studying this poorly understood program of development. Leeches are also used for the study of segmentation, regeneration and neurogenesis.

Protocols are provided for Handling Embryos, Microinjection, Devitellinization, Silver Staining, Immunohistochemistry, In Situ Hybridization, and Preparation for Microscopy.

For more emerging (and re-emerging) model systems, these articles and others like them are collected in Volume 1 of a new laboratory manual series.

Our series highlighting new and lesser-known laboratory model organisms continues in February, with two sets of articles detailing the use of moss and choanoflagellates.

The moss Physcomitrella patens has been used in laboratory research for more than 80 years, but the last 15 have seen a resurgence in moss research. P. patens can easily be grown in the lab, and spends most of its life in a haploid state that allows many of the approaches used in yeast and microbes to be applied. Methods for RNAi have been worked out, the genome has been sequenced and assembled, physical and genetic maps are available, and more than 250,000 expressed sequence tags (ESTs) are known. Ralph Quatrano and colleagues have contributed an overview of the use of P. patens as a laboratory organism to February’s issue of Cold Spring Harbor Protocols along with protocols for culture, isolation of protoplasts, somatic hybridization, chemical and UV mutagenesis, transformation via direct DNA uptake, T-DNA mutagenesis, and biolistic delivery systems, and isolation of DNA, RNA and proteins.

Choanoflagellates are a varied group of protozoa that are the closest living relative to the metazoa, and their study is leading to new insights into metazoan ancestry and origins. Barry Leadbeater and colleagues have written up a series of articles highlighting the use of Monosiga brevicollis as a representative species, as it has recently had its genome sequenced, and is readily grown and manipulated in the laboratory (protocols included are generally transferable to most choanoflagellate species). The set of articles includes an overview of choanoflagellates, and protocols for isolation from field samples and culture of choanoflagellates, long-term storage, visualization of actin and beta-tubulin, purification of total RNA, and preps for rapid DNA isolation, high molecular weight DNA isolation and separation of choanoflagellate and bacterial genomic DNA.

These articles on Emerging Model Organisms are being collected in a series of lab manuals, the first of which is currently available here (now on sale 25% off!).

Our series on emerging model organisms continues this month, bringing you a set of articles on two systems that may be new to you, and one that’s a long-time classic.

Marianne Bronner-Fraser and colleagues have written up a guide to using the Sea Lamprey, Petromyzon marinus in the laboratory. The unique evolutionary position of the lamprey makes it a fascinating animal for comparative studies, and there are also lamprey-specific systems that are being investigated, like its variable lymphocyte receptor-mediated immune system. Protocols for culturing embryos, microinjection of RNA and morpholinos, DiI cell labeling, whole-mount in situ hybridization and immunohistochemistry are available.

Nipam Patel’s group at Berkeley brings us a look at the amphipod crustacean Parhyale hawaiensis. This crustacean is extremely amenable to laboratory studies, producing large amounts of embryos year round. The establishment of the segemented body plan is a particular area of interest for studies of P. hawaiensis. Protocols are provided for fixing and dissecting embryos, injection with fluorescent dyes, antibody staining and in situ hybridization.

Rusty Lansford and colleagues have written up their methods for using the classic developmental biology system, the Japanese Quail, Coturnix coturnix japonica. Their transgenic system is a big breakthrough, and deserves its own blog article, which I’ll post next week.

Just back in from the ASCB meeting, so much to catch up on. But I thought I’d be remiss if I didn’t highlight the set of emerging model organisms featured in this month’s issue of Cold Spring Harbor Protocols:
The Demosponge Amphimedon queenslandica is the first poriferan to have its genome sequenced, assembled and annotated and it represents one of the most (if not the most) ancient phyla of multicellular animals alive today. Protocols are provided for isolation of embryos, in situ hybridization, cell labeling and tracking, and genotyping.

Dictyostelium discoideum, known as “The Social Ameba” has a long history in scientific research, and is more a “classic” system than an emerging one. A unicellular eukaryote, D. discoideum can form a multicellular structure when nutrient conditions are limiting. The cellular and molecular aspects of their multicellular lifestyle have been studied in detail, and general principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from this work and have been found to be conserved across all eukaryotes. Protocols are provided for growth, multicellular development, making stocks, transformation, electroporation, selection of transformants, DNA extraction, and RNA extraction.

The Two-Spotted Cricket Gryllus bimaculatus has been widely used to study insect physiology and neurobiology. Its capacity for regeneration and amenability toward RNAi-based methods makes it an excellent system for the study of development and regeneration.

The Dogfish Scyliorhinus canicula is a relatively small shark that is fairly easy to maintain in the laboratory. It provides a window into the oft-neglected (due to technical difficulties) study of chondrichthyans, which should provide valuable insight due to their evolutionary position. It also allows anaylsis of the elaborate physiological and sensory systems used by sharks.